Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding

The duplicated and the highly repetitive nature of the maize genome has historically impeded the development of true single nucleotide polymorphism (SNP) markers in this crop. Recent advances in genome complexity reduction methods coupled with sequencing-by-synthesis technologies permit the implementation of efficient genome-wide SNP discovery in maize. In this study, we have applied Complexity Reduction of Polymorphic Sequences technology (Keygene N.V., Wageningen, The Netherlands) for the identification of informative SNPs between two genetically distinct maize inbred lines of North and South American origins. This approach resulted in the discovery of 1,123 putative SNPs representing low and single copy loci. In silico and experimental (Illumina GoldenGate (GG) assay) validation of putative SNPs resulted in mapping of 604 markers, out of which 188 SNPs represented 43 haplotype blocks distributed across all ten chromosomes. We have determined and clearly stated a specific combination of stringent criteria (>0.3 minor allele frequency, >0.8 GenTrainScore and >0.5 Chi_test100 score) necessary for the identification of highly polymorphic and genetically stable SNP markers. Due to these criteria, we identified a subset of 120 high-quality SNP markers to leverage in GG assay-based marker-assisted selection projects. A total of 32 high-quality SNPs represented 21 haplotypes out of 43 identified in this study. The information on the selection criteria of highly polymorphic SNPs in a complex genome such as maize and the public availability of these SNP assays will be of great value for the maize molecular genetics and breeding community.     

蛋白激酶C对鼻咽癌细胞c－myc，c－fos表达的影响

用蛋白激酶Ｃ（ＰＫＣ）抑制剂Ｓｔａｕｒｏｓｐｏｒｉｎｅ（ＳＴ,抑制催化亚基）与Ｓｐｈｉｎｇｏｓｉｎｅ（ＳＳ,抑制调节亚基）处理人鼻咽癌细胞系ＣＮＥ－２Ｚ,经点印迹后扫描定量和免疫细胞化学检测ｃ－ｍｙｃ、ｃ－ｆｏｓ表达及其分布。结果发现：（１）ｃ－ｍｙｃ蛋白：主要分布于胞浆,４０．７％的细胞核与胞浆均为阳性;经ＳＳ或ＳＴ处理后,表达明显减弱,且核阳性率分别为１７．３％与２３．３％。扫描定量在ＳＳ组为对照组的６０％±２５．７％（Ｐ＜０．０５）,ＳＴ组为对照组的５５％±２５．９％（Ｐ＜０．０５）。（２）Ｃ－ｆｏｓ蛋白：主要分布于胞浆,２９．４％的细胞核与胞浆均为阳性,经ＳＳ或ＳＴ处理后,表达明显减弱,且核阳性率分别为９％与１０．２％。扫描定量ＳＳ组为对照组的５８．６％±２５％（Ｐ＜０．０５）,ＳＴ组为对照组的５９．７％±２６．２％（Ｐ＜０．０５）。结果表明：使用ＰＫＣ抑制剂后,两种核癌基因产物量均有不同程度的减少,并且存在细胞内分布的改变,特别是其发挥效应的核内表达明显减少。结合我们以前所发现的ＰＫＣ抑制剂明显抑制ＣＮＥ—２Ｚ细胞生长的结果,提示这些癌基因可能参与了ＰＫＣ对ＣＮＥ—２Ｚ细胞生长的调节。     

Mechanistic evaluation of virus clearance by depth filtration

Virus clearance by depth filtration has not been well‐understood mechanistically due to lack of quantitative data on filter charge characteristics and absence of systematic studies. It is generally believed that both electrostatic interactions and sized based mechanical entrapment contribute to virus clearance by depth filtration. In order to establish whether the effectiveness of virus clearance correlates with the charge characteristics of a given depth filter, a counter‐ion displacement technique was employed to determine the ionic capacity for several depth filters. Two depth filters (Millipore B1HC and X0HC) with significant differences in ionic capacities were selected and evaluated for their ability to eliminate viruses. The high ionic capacity X0HC filter showed complete porcine parvovirus (PPV) clearance (eliminating the spiked viruses to below the limit of detection) under low conductivity conditions (≤2.5 mS/cm), achieving a log₁₀ reduction factor (LRF) of > 4.8. On the other hand, the low ionic capacity B1HC filter achieved only ～2.1–3.0 LRF of PPV clearance under the same conditions. These results indicate that parvovirus clearance by these two depth filters are mainly achieved via electrostatic interactions between the filters and PPV. When much larger xenotropic murine leukemia virus (XMuLV) was used as the model virus, complete retrovirus clearance was obtained under all conditions evaluated for both depth filters, suggesting the involvement of mechanisms other than just electrostatic interactions in XMuLV clearance. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 31:431–437, 2015     

Effects of resuspension and eutrophication level on summer phytoplankton dynamics in two hypertrophic areas of Lake Taihu,China

The composition of summer phytoplankton communities in two highly eutrophic areas of Lake Taihu, a large, shallow water body in China (area 2,338 km²; mean depth 2.0 m), was studied in relation to selected environmental variables. Both areas have multiple uses, including drinking water supply, fisheries, and recreation. The first area, Meiliang Bay, is much closer to central lake and subjected to wind-driven sediment resuspension, while the second, at Wuli Lake, is less affected by wave action but is considered more nutrient-rich due to its proximity to human inhabitation. By comparing two lake areas, we attempt to advance the understanding and management of different regions of shallow lakes, mainly differing in resuspension levels and eutrophication levels. A comparison of these two lake areas indicated a higher standing crop of phytoplankton in Wuli Lake than in Meiliang Bay. Canonic Correspondence Analysis indicated that nutrient status and sediment resuspension were the principal factors influencing phytoplankton composition in both areas. The dominant algal group in Meiliang Bay comprised immobile R-type strategists (Reynolds in Growth and reproductive strategies of freshwater phytoplankton, 1988), including filamentous diatoms and green algae (Aulacoseira granulate and Planctonema lauterbornii), and recruitment-beneficial RS-type strategists, mainly the colonial cyanobacteria (Microcystis spp.). The community of Wuli Lake was dominated by S-strategists, principally motile flagellates (Cryptomonas spp.) and C-strategists including small nonmotile centric diatoms and chlorococcal green algae.     

Microwave-assisted Nile red method for in vivo quantification of neutral lipids in microalgae

In vivo determination of neutral lipids with Nile red fluorescence has been used as a rapid screening method for certain types of microalgae, but has been unsuccessful in others, particularly those with thick, rigid cell walls that prevent penetration of the fluorescence dye into the cell. To solve the problem, a microwave-assisted Nile red staining method for microalgal lipid determination was developed. In a two-step staining protocol, 50 and 60 s were selected as the optimal microwave times for the pretreatment and staining process, respectively. Moreover, several calibration methods for quantitative analysis of neutral lipids in microalgae were investigated and compared with conventional gravimetric methods. Factors that affected the in vivo quantification of cellular neutral lipids were also investigated. Application of the new method for detection and quantification of neutral lipids in a number of green microalgae was demonstrated.     

Analysis of variable sites between two complete South China tiger (Panthera tigris amoyensis) mitochondrial genomes

In order to investigate the mitochondrial genome of Panthera tigris amoyensis, two South China tigers (P25 and P27) were analyzed following 15 cymt-specific primer sets. The entire mtDNA sequence was found to be 16,957 bp and 17,001 bp long for P25 and P27 respectively, and this difference in length between P25 and P27 occurred in the number of tandem repeats in the RS-3 segment of the control region. The structural characteristics of complete P. t. amoyensis mitochondrial genomes were also highly similar to those of P. uncia. Additionally, the rate of point mutation was only 0.3% and a total of 59 variable sites between P25 and P27 were found. Out of the 59 variable sites, 6 were located in 6 different tRNA genes, 6 in the 2 rRNA genes, 7 in non-coding regions (one located between tRNA-Asn and tRNA-Tyr and six in the D-loop), and 40 in 10 protein-coding genes. COI held the largest amount of variable sites (9 sites) and Cytb contained the highest variable rate (0.7%) in the complete sequences. Moreover, out of the 40 variable sites located in 10 protein-coding genes, 12 sites were nonsynonymous.     

地上部植食者褐飞虱对不同水稻品种土壤线虫群落的影响

地上和地下部生物群落的交互作用对于调控陆地生态过程具有重要作用。在盆栽条件下利用2×2析因设计研究了褐飞虱(Nilaparvata lugens)取食不同水稻品种后对土壤线虫群落的影响。结果表明, 褐飞虱侵害水稻9 d后, 感虫品种(广四和汕优63)的土壤线虫总数、属数及自生线虫(食细菌线虫、食真菌线虫和捕食性线虫)数量增加, 并且一般达到显著水平(P<0.05); 而上述指标在抗虫品种(汕优559和IR36)土壤中则呈现相反的趋势。植食性线虫数量在强感虫品种广四上显著增加(P<0.05), 而在强抗虫品种IR36上显著减少(P<0.05)。褐飞虱和水稻品种对土壤线虫的生态指数(线虫通道指数、Shannon-Wiener指数、成熟度指数、富集指数和结构指数)没有明显影响, 可能与供试土壤线虫群落组成单一及褐飞虱作用时间较短有关。总之, 褐飞虱强烈影响土壤线虫数量、群落组成和营养结构, 并且作用的方向(促进或抑制)和程度依赖于水稻的品种特性, 揭示出地上部植食者的短期侵害将对稻田土壤生态系统的结构和功能产生深远影响。     

Leaf chlorophyll content as a proxy for leaf photosynthetic capacity

Improving the accuracy of estimates of forest carbon exchange is a central priority for understanding ecosystem response to increased atmospheric CO₂ levels and improving carbon cycle modelling. However, the spatially continuous parameterization of photosynthetic capacity (Vcmax) at global scales and appropriate temporal intervals within terrestrial biosphere models (TBMs) remains unresolved. This research investigates the use of biochemical parameters for modelling leaf photosynthetic capacity within a deciduous forest. Particular attention is given to the impacts of seasonality on both leaf biophysical variables and physiological processes, and their interdependent relationships. Four deciduous tree species were sampled across three growing seasons (2013–2015), approximately every 10 days for leaf chlorophyll content (Chl_Leaf) and canopy structure. Leaf nitrogen (N_Area) was also measured during 2014. Leaf photosynthesis was measured during 2014–2015 using a Li‐6400 gas‐exchange system, with A‐Ci curves to model Vcmax. Results showed that seasonality and variations between species resulted in weak relationships between Vcmax normalized to 25°C () and N_Area (R² = 0.62, P < 0.001), whereas Chl_Leaf demonstrated a much stronger correlation with (R² = 0.78, P < 0.001). The relationship between Chl_Leaf and N_Area was also weak (R² = 0.47, P < 0.001), possibly due to the dynamic partitioning of nitrogen, between and within photosynthetic and nonphotosynthetic fractions. The spatial and temporal variability of was mapped using Landsat TM/ETM satellite data across the forest site, using physical models to derive Chl_Leaf. TBMs largely treat photosynthetic parameters as either fixed constants or varying according to leaf nitrogen content. This research challenges assumptions that simple N_Area– relationships can reliably be used to constrain photosynthetic capacity in TBMs, even within the same plant functional type. It is suggested that Chl_Leaf provides a more accurate, direct proxy for and is also more easily retrievable from satellite data. These results have important implications for carbon modelling within deciduous ecosystems.